Despite many breakthroughs in cardiovascular medicine, the treatment of ischemic cardiovascular diseases remains among the most prominent health challenges worldwide. The identification of adult stem or progenitor cells capable of contributing to tissue regeneration has raised the possibility that cell therapy could be employed for repair of ischemic damaged tissues. Current investigations have suggested bone marrow (BM) cells as a potential source for adult stem or progenitor cells. BM-derived stem cells appear to have the capacity to repopulate many nonhematopoietic tissues, such as vessel and muscle. The promising results from initial experimental studies on BM-derived stem cells have already promoted the initiation of clinical trials for the treatment of acute myocardial infarction, ischemic cardiomyopathy, and limb ischemia. Yet knowledge relating to adult stem cells populations is incomplete. One of the most important and unresolved issues in cell therapy is the selection of ideal cells for regeneration. Even though various kinds of stem or progenitor cells have been proposed and shown to be effective for cardiovascular regeneration, each cell type has its own pitfalls. For example, un-fractionated whole BM cells may encounter unexpected and potentially serious adverse effects, such as intramyocardial calcification. CD34+ cells or c-kit+ cells exist in low numbers in BM (less than 1%), therefore, the mobilization process is required to obtain sufficient numbers of cells to be used for cell therapy. Endothelial progenitor cells or mesenchymal stem cells are culture expandable cells, that require large amounts of serum for culture and need from days to months to be prepared for clinical use. Better methods for selecting, isolating, and culturing stem cells for use in regenerative medicine are urgently required.